Related papers: Model chromatin flows: numerical analysis of linea…
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
The genome contains genetic information essential for cell's life. The genome's spatial organization inside the cell nucleus is critical for its proper function including gene regulation. The two major genomic compartments -- euchromatin…
Motivated by chromosomes enclosed in nucleus and the recently discovered active topological glass, we study a spherically confined melt of long nonconcatenated active polymer rings. Without activity, the rings exhibit the same average…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…
Active polymers are ubiquitous in nature, and often kicked by persistent noises that break detailed balance. In order to capture the out-of-equilibrium dynamics of such active polymers, we propose a simple yet reliable analytical framework…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
\textbf{Purpose:} This paper addresses long-standing solar physics problems, namely, the heating of the solar chromosphere and the origin of the solar wind. Our aim is to reveal the related mechanisms behind chromospheric heating and plasma…
Heterogeneous distribution of passive and active domains in the chromosome plays a crucial role for its dynamic organization within the cell nucleus. Motivated by that here we investigate the steady-state conformation and dynamics of a…
Recent experimental studies have shown that confinement can profoundly affect self-organization in semi-dilute active suspensions, leading to striking features such as the formation of steady and spontaneous vortices in circular domains and…
We theoretically describe the dynamics of swimmer populations confined in thin liquid films. We first demonstrate that hydrodynamic interactions between confined swimmers only depend on their shape and are independent of their specific…
Mechanochemical patterns arising in the actomyosin cortex drive many cellular processes. Here we consider a hydrodynamic model for the actomyosin cortex of cells and study the sensitivity of the emergent patterns to both physical parameters…
Swimming micro-organisms such as bacteria or spermatozoa are typically found in dense suspensions, and exhibit collective modes of locomotion qualitatively different from that displayed by isolated cells. In the dilute limit where…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…
Generic interacting many-body quantum systems are believed to behave as classical fluids on long time and length scales. Due to rapid progress in growing exceptionally pure crystals, we are now able to experimentally observe this collective…
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such…
Using agent-based simulations of self-propelled particles subject to short-range repulsion and nematic alignment we explore the dynamical phases of a dense active material confined to the surface of a sphere. We map the dynamical phase…
Recent experiments on active materials, such as dense bacterial suspensions and microtubule-kinesin motor mixtures, show a promising potential for achieving self-sustained flows. However, to develop active microfluidics it is necessary to…